CDCA7

cell division cycle associated 7

Basic information

Region (hg38): 2:173354819-173368997

Links

ENSG00000144354 ∙ NCBI:83879 ∙ OMIM:609937 ∙ HGNC:14628 ∙ Uniprot:Q9BWT1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency-centromeric instability-facial anomalies syndrome 3 (Strong), mode of inheritance: AR
• immunodeficiency-centromeric instability-facial anomalies syndrome (Supportive), mode of inheritance: AR
• immunodeficiency-centromeric instability-facial anomalies syndrome 3 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency-centromeric instability-facial anomalies syndrome 3	AR	Allergy/Immunology/Infectious	Individuals have been described with recurrent childhood infections, and awareness may allow prompt and aggressive treatment of infections	Allergy/Immunology/Infectious; Craniofacial; Gastrointestinal; Neurologic	15952214; 1999836; 26216346

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDCA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDCA7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	54	6	62
missense		2	84	2		88
nonsense			4			4
start loss						0
frameshift			3			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)			2			2
splice region			4	14		18
non coding			2	31	9	42
Total	0	2	99	87	15

Variants in CDCA7

This is a list of pathogenic ClinVar variants found in the CDCA7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-173354970-G-A			Uncertain significance (May 12, 2022)
2-173354978-C-T			Likely benign (May 24, 2023)
2-173354979-G-A			Uncertain significance (Jul 30, 2022)
2-173354981-G-A			Likely benign (Nov 20, 2022)
2-173354987-G-A			Uncertain significance (Jun 02, 2022)
2-173354996-G-A			Likely benign (May 02, 2023)
2-173354997-C-T			Uncertain significance (Jan 14, 2021)
2-173354998-G-A			Likely benign (Jan 12, 2024)
2-173355004-A-G			Likely benign (Jun 05, 2021)
2-173358695-G-A			Likely benign (Aug 10, 2023)
2-173358695-G-T			Benign (Jan 25, 2024)
2-173358697-T-C			Likely benign (Jan 27, 2021)
2-173358711-G-A			Uncertain significance (Jul 12, 2022)
2-173358729-AAAG-A			Uncertain significance (Jun 12, 2022)
2-173358735-G-A			Likely benign (Jan 01, 2024)
2-173358763-T-C			Likely benign (Sep 28, 2022)
2-173358783-G-A			Likely benign (Nov 12, 2023)
2-173358807-C-T			Likely benign (Jul 12, 2023)
2-173358816-T-C			Likely benign (Oct 13, 2023)
2-173358836-C-T			Uncertain significance (Dec 11, 2023)
2-173358845-CT-C			Likely benign (Jun 10, 2022)
2-173358848-C-T			Likely benign (Dec 21, 2023)
2-173358851-G-A			Likely benign (Dec 30, 2023)
2-173358852-A-C			Likely benign (Jan 26, 2023)
2-173358854-A-G			Likely benign (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDCA7	protein_coding	protein_coding	ENST00000306721	10	14178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0108	0.989	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	203	277	0.732	0.0000172	2959
Missense in Polyphen		69	106.7	0.64665		1222
Synonymous	1.73	80	102	0.782	0.00000640	847
Loss of Function	3.12	8	24.8	0.323	0.00000147	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000515	0.000514
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in MYC-mediated cell transformation and apoptosis; induces anchorage-independent growth and clonogenicity in lymphoblastoid cells. Insufficient to induce tumorigenicity when overexpressed but contributes to MYC-mediated tumorigenesis. May play a role as transcriptional regulator. {ECO:0000269|PubMed:11598121, ECO:0000269|PubMed:15994934, ECO:0000269|PubMed:16580749, ECO:0000269|PubMed:23166294}.
• Disease: DISEASE: Immunodeficiency-centromeric instability-facial anomalies syndrome 3 (ICF3) [MIM:616910]: A rare disorder characterized by a variable immunodeficiency resulting in recurrent infections, facial anomalies, and branching of chromosomes 1, 9, and 16. Other variable symptoms include growth retardation, failure to thrive, and psychomotor retardation. Laboratory studies show limited hypomethylation of DNA in a small fraction of the genome in some, but not all, patients. {ECO:0000269|PubMed:26216346}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
• Pathway: Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.734
• rvis_EVS: -0.69
• rvis_percentile_EVS: 14.97

Haploinsufficiency Scores

• pHI: 0.422
• hipred: N
• hipred_score: 0.357
• ghis: 0.686

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.419

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cdca7

Zebrafish Information Network

• Gene name: cdca7a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: regulation of transcription, DNA-templated;apoptotic process;regulation of cell population proliferation
• Cellular component: nucleus;nucleoplasm;cytosol